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| Status |
Public on Apr 30, 2019 |
| Title |
naïve LPM input DNA |
| Sample type |
SRA |
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| Source name |
Peritoneal lavage
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
treatment: untreated
tx conditions: NA
cell type: LPM
chip antibody: none
gender: male
|
| Treatment protocol |
See above
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bhlhe40 immunoprecipitation of bound, crosslinked DNA from LPMs
Genome Technology Access core (WUSTL)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
NA
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| Data processing |
FASTQ quality control, FastQC (0.11.3)
Read mapping, Bowtie (1.1.1) (mm10 reference genome)
Peak calling, MACS v1.4 (relative to input controls)
Peaks from unmapped regions and/or with fold-enrichment <5 were excluded
Normalized track generation, Deeptools (2.5.3)
Genome_build: Peak annotation, R package ChIPseeker (1.14.1)
Supplementary_files_format_and_content: bed, peaks, bw
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| Submission date |
Jan 28, 2019 |
| Last update date |
May 01, 2019 |
| Contact name |
Brian T Edelson |
| E-mail(s) |
bedelson@path.wustl.edu
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| Organization name |
Washington University in St. Louis
|
| Department |
Pathology and Immunology
|
| Lab |
Rm. 8304
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| Street address |
425 S. Euclid Ave.
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| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
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| Platform ID |
GPL21493 |
| Series (2) |
| GSE125729 |
Chromatin immunoprecipitation sequencing (ChIP-Seq) for Bhlhe40 from naïve and IL-4c-stimulated large peritoneal macrophages (LPMs) |
| GSE125730 |
Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity |
|
| Relations |
| BioSample |
SAMN10829919 |
| SRA |
SRX5299297 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3581127_naive_input_depth_norm.bw |
171.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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